Hi Douglas and Bruce,

I have updated my freesurfer version to 5.0.0. But I still have error when I tried to run bbregister. The error information is as follows"

My command: bbregister --s bert --mov T2_0145_file1.nii --reg register.dat --init-fsl --t2 --o outvol

Error information:

FREESURFER_HOME /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
$Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
reading from T2_0145_file1.nii...
TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999276, 0, 0.0380414)
j_ras = (-0.00161026, 0.999104, -0.0422986)
k_ras = (0.0380073, 0.0423292, 0.998381)
writing to ./tmp.bbregister.16142/template.nii...
fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.16142/fslregister --dof 6
ERROR: Flag --niters unrecognized.

I am not sure about the reason since the Flag --niters seems to be created during the process, but not in my original command.

I would be most grateful if you could help me solve this problem.

Thanks in advance.

Best,
Xiaoying


2011/5/22 Xiaoying Tang <xtang7@jhu.edu>
The full name on my machine is: freesurfer-centos4_x86_64-v4.1.0

So I think the version is 4.1.0

Best,
Xiaoying

2011/5/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
No, it's not the same what version are you running?



On May 21, 2011, at 11:26 PM, Xiaoying Tang <xtang7@jhu.edu> wrote:

Hi Douglas,

Thanks a lot for your suggestion.

It is really strange that I don't find bbregister in the file foler of the freesurfer on my machine. But I find a program named "fslregister". Is that the same? 

If they are different, is it that I need to update my version of freesurfer so that I can have the program bbregister?

Thanks a lot.

Best,
Xiaoying

2011/5/21 Douglas Greve <greve@nmr.mgh.harvard.edu>
If you have a T1 that you've run through FS and are happy with the skull
strip, then you can register your T2 with the FS anatomical (with
bbregister), then map the skull stripped T1 into the T2 space
(mri_vol2vol), then apply it to the T2 (mri_mask).

doug

On 5/21/11 7:27 PM, Bruce Fischl wrote:
> Hi Xiaoying,
>
> unfortunately there isn't. I would recommend BET (from the FSL).
>
> cheers
> Bruce
> On Sat, 21 May 2011,
> Xiaoying Tang wrote:
>
>> Hi All,
>>
>> I am wondering whether there is any way to skull strip a T2 image using
>> freesurfer. I tried to use the same way as for skullstripping T1 image, but
>> always failed.
>>
>> I would be most grateful if someone can give me some suggestion.
>>
>> Best,
>> Xiaoying Tang
>>
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